JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. If was developed by Guillaume Marçais and Carl Kingsford. You can find more information on JellyFish [[http://​www.cbcb.umd.edu/​software/​jellyfish/​|here]].

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. If was developed by Guillaume Marçais and Carl Kingsford. You can find more information on JellyFish [[http://​www.cbcb.umd.edu/​software/​jellyfish/​|here]].

+

+

====Enivironment Setup====

+

+

To work with jellyfish first we need to load the module. The easiest way to do this is to modify the ''​.bashrc''​ file in your ''​$HOME''​ directory.

+

+

<​code>​

+

module load jellyfish

+

</​code>​

+

+

Then in your ''​$HOME''​ directory create another directory to submit your jellyfish jobs, and copy the ''​fasta''​ data file we will be using for the test job into the new directory.

To run the example job create a ''​PBS''​ script in the directory where you will submit the job and that has the necessary ''​fasta''​ file. The script will look like the one below.

+

+

<​code>​

+

#!/bin/bash

+

#PBS -N jellyfish

+

#PBS -q tiny12core

+

#PBS -j oe

+

#PBS -o jellyfish.$PBS_JOBID

+

#PBS -l nodes=1:​ppn=12

+

#PBS -l walltime=1:​00:​00

+

+

cd $PBS_O_WORKDIR

+

cp seq10m.fa ​ /​scratch/​$PBS_JOBID

+

cd /​scratch/​$PBS_JOBID

+

+

jellyfish count -m 10 -o output -c 3 -s 10000000 -t 12 seq10m.fa

+

cp output $PBS_O_WORKDIR

+

</​code>​

+

+

This will give us an ''​output''​ hash file that we can process with jellyfish. For more information on the flags we used see the manual [[http://​www.cbcb.umd.edu/​software/​jellyfish/​jellyfish-manual-1.1.pdf|here]].

+

+

All thats left is to submit the job.

+

+

<​code>​

+

razor-l3:​jokinsey:​~/​JELLYFISH-JOBS$ qsub jellyfish.pbs ​

+

</​code>​

+

+

Once we have the ''​output''​ hash we can run other jellyfish operations with is like the ''​histo''​ operation shown below, which might be a way to verify your ''​output''​.